Why no java script?

I've customized my CSS and gotten my theme looking exactly the way I want it. I am using the template to re-do my regular website's online store, since it is way easier to design in WordPress than to do it from scratch!

However, I just changed over to a new shopping cart system to get away from having a pop-up cart (which is blocked by many customers' browsers). The new (non-popping) cart requires java script. Why isn't java allowed in WordPress? I'm not putting shopping cart buttons into a widget or sidebar--just straight in the code of each page.

I'm curious to know if this is a policy with a serious "why" to it, or if it's something WordPress would reconsider -- or if there's already a way to put java buttons into the page that I just don't know about.